changed year to 2021

README.md

@@ -147,13 +147,13 @@ This last step requires a preceeding `docker login`. Ask Jannick for login crede
 ## Code structure
 **WARNING: is not created automatically - might be out of date!**
 Reverse engineered plantuml diagram of the current code structure: 
-![Can't load image](doc/KiT-RT.svg "UML diagram")
+![Can't load image](doc/images/uml.svg "UML diagram")
 <br/><br/>
 Was created using [hpp2plantuml](https://github.com/thibaultmarin/hpp2plantuml) and [plantuml](https://plantuml.com/), e.g.:
 ```bash
 cd doc 
-hpp2plantuml -i "../code/include/*.h" -i "../code/include/*/*.h" -o KiT-RT.puml
-plantuml KiT-RT.puml -tsvg
+hpp2plantuml -i "../code/include/*.h" -i "../code/include/*/*.h" -o uml.puml
+plantuml uml.puml -tsvg
 ```
 
 ---

doc/_static/theme_overrides.css

+.wy-side-nav-search {
+    background-color: #343131;
+}

doc/common/config.rst

+Class Config
+============
+
+.. doxygenclass:: Config
+   :members:

doc/common/index.rst

+Common
+======
+
+TODO
+
+.. toctree::
+   :maxdepth: 1
+
+   config
+   mesh

doc/common/mesh.rst

+Class Mesh
+==========
+
+.. doxygenclass:: Mesh
+    :members:

doc/conf.py

 import subprocess, os
 
-# Configuration file for the Sphinx documentation builder.
-#
-# This file only contains a selection of the most common options. For a full
-# list see the documentation:
-# https://www.sphinx-doc.org/en/master/usage/configuration.html
-
-# -- Path setup --------------------------------------------------------------
-
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
-#
-# import os
-# import sys
-# sys.path.insert(0, os.path.abspath('.'))
-
-
-# -- Project information -----------------------------------------------------
-
 project = 'KiT-RT'
-copyright = '2020, TBD'
-author = 'TBD'
-
-# The full version, including alpha/beta/rc tags
-release = '0.1'
+copyright = '2021, Karlsruhe Institute of Technology'
+author = 'Jonas Kusch, Steffen Schotthöfer, Pia Stammer, Jannick Wolters, Tianbai Xiao'
 
+version = 'v0.1'
+release = 'v0.1'
 
-# -- General configuration ---------------------------------------------------
 
-# Add any Sphinx extension module names here, as strings. They can be
-# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
-# ones.
 extensions = [
     'sphinx.ext.autodoc',
     'sphinx.ext.napoleon',
@@ -42,30 +18,20 @@ extensions = [
     'sphinx_rtd_theme'
 ]
 
-# Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
-
-# The master toctree document.
+#templates_path = ['_templates']
 master_doc = 'index'
-
-# List of patterns, relative to source directory, that match files and
-# directories to ignore when looking for source files.
-# This pattern also affects html_static_path and html_extra_path.
 exclude_patterns = []
 
-
-# -- Options for HTML output -------------------------------------------------
-
-# The theme to use for HTML and HTML Help pages.  See the documentation for
-# a list of builtin themes.
-#
-html_theme = "sphinx_rtd_theme"
-
-# Add any paths that contain custom static files (such as style sheets) here,
-# relative to this directory. They are copied after the builtin static files,
-# so a file named "default.css" will overwrite the builtin "default.css".
+html_theme = 'sphinx_rtd_theme'
+html_theme_options = {
+    'logo_only': True,
+    'display_version': True,
+}
+html_logo = 'images/KiT-RT_logo_small.png'
 html_static_path = ['_static']
-"""
+def setup(app):
+    app.add_css_file('theme_overrides.css')
+
 breathe_projects = {
     "KiT-RT": "../code/build/debug/docs/doxygen/xml/",
 }
@@ -86,4 +52,3 @@ if read_the_docs_build:
                 line = line.replace('@DOXYGEN_INPUT_DIR@', inputDir)
                 fout.write(line)
     subprocess.call('doxygen', shell=True)
-"""
\ No newline at end of file

doc/cpp_doc.rst

+C++ Documentation
+=================
+
+.. image:: images/uml.svg
+  :width: 800
+  :alt: UML diagram
+
+.. toctree::
+   :maxdepth: 2
+   
+   common/index
+   entropies/index
+   fluxes/index
+   kernels/index
+   optimizers/index
+   problems/index
+   quadratures/index
+   solvers/index
+   toolboxes/index

doc/guide_developer.rst → doc/developer_guide.rst

 ================
-Guidance
+Developer Guide
 ================
 

doc/entropies/index.rst

+Entropies
+=========
+
+TODO
+
+.. toctree::
+   :maxdepth: 1
\ No newline at end of file

doc/fluxes/index.rst

+Fluxes
+======
+
+TODO
+
+.. toctree::
+   :maxdepth: 1
\ No newline at end of file

doc/index.rst

-.. KiT-RT documentation master file, created by
-   sphinx-quickstart on Mon Nov 30 16:55:47 2020.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
+===========================================================
+KiT-RT - The kinetic transport solver for radiation therapy
+===========================================================
 
-Welcome to KiT-RT's documentation!
-==================================
+The KiT-RT framework is a powerful open source platform for radiation transport. Its main focus is on radiotherapy planning in cancer treatment. To allow problem-specific method selection, the framework provides different deterministic solver types. This not only facilitates treatment planning, but also provides tools to investigate various research questions in the field of radiative transfer. This goal is supported by an easily extensible code structure that allows straightforward implementation of additional methods and techniques.
+
+The software is being developed by members of the group `CSMM <https://www.scc.kit.edu/forschung/13971.php?tab=%5B14114%5D#tabpanel-14114>`_ at the Karlsruhe Institute of Technology (KIT). For more information, please contact any of our authors (link to authors page).
+   
+--------
+Contents
+--------
 
 .. toctree::
    :maxdepth: 1
-   :caption: Contents:
-   introduction
-   authors
+  
    installation
+   physics
    configFiles
+   cpp_doc
+   developer_guide
+   release
+   authors
    philosophy
-
-
-Docs
-====
-
-.. doxygenclass:: Mesh
-   :members:

doc/introduction.rst

-.. _introduction:
-
-KiT-RT - The kinetic transport solver for radiation therapy 
----------------------------------------------
-
-The KiT-RT framework is a powerful open source platform for radiation transport. Its main focus is on radiotherapy planning in cancer treatment. To allow problem-specific method selection, the framework provides different deterministic solver types. This not only facilitates treatment planning, but also provides tools to investigate various research questions in the field of radiative transfer. This goal is supported by an easily extensible code structure that allows straightforward implementation of additional methods and techniques.
-
-The software is being developed by members of the group `CSMM <https://www.scc.kit.edu/forschung/13971.php?tab=%5B14114%5D#tabpanel-14114>`_ at the Karlsruhe Institute of Technology (KIT). For more information, please contact any of our authors (link to authors page).

doc/kernels/index.rst

+Kernels
+=======
+
+TODO
+
+.. toctree::
+   :maxdepth: 1
\ No newline at end of file

doc/optimizers/index.rst

+Optimizers
+==========
+
+TODO
+
+.. toctree::
+   :maxdepth: 1
\ No newline at end of file

doc/problems/index.rst

+Problems
+========
+
+TODO
+
+.. toctree::
+   :maxdepth: 1
\ No newline at end of file

doc/quadratures/index.rst

+Quadratures
+===========
+
+TODO
+
+.. toctree::